Peptide Based Self-assembled Systems: Structures and Applications

Mondal, Sahabaj (2023) Peptide Based Self-assembled Systems: Structures and Applications. PhD thesis, Indian Institute of Science Education and Research Kolkata.

Text (PhD thesis of Sahabaj Mondal (18RS111)) 18RS111.pdf - Submitted Version Restricted to Repository staff only Download (18MB)

Abstract

This thesis entitled as “Peptide Based Self-assembled Systems: Structures and Applications” is all about the design, synthesis, characterization, self-assembly and application of peptide based molecules using proteinogenic and/or non-coded amino acids. The main focus of this thesis is to develop synthetic peptides or Peptide mimetics composed of both genetically coded and non-coded amino acids for studying and understanding the molecular self-assembly processes of these peptides in supramolecular helices, sheets and to study their further aggregation behavior in forming gels or nanomaterials like tube, vesicle, fibre, porous structure and their versatile applications in several fields. The aggregation of proteins and peptides into fibrils is associated with many neurodegenerative diseases in humans, including Alzheimer’s disease, Parkinson’s disease and non-neurological type-II diabetes. A better understanding of the fibril formation process and defibrillation using biochemical tools is highly important for therapeutics. Under physiological conditions, acidic pH promotes the formation of toxic fibrils. Here, a mimic of living systems has been achieved by the acid-responsive assembly of benzyloxycarbonyl-L-phenylalanine to fibrils, as well as the urease-assisted disassembly of the said fibrils. The simultaneous incorporation of the two triggers helped to prepare a transient supramolecular hydrogel from benzyloxycarbonyl-L-phenylalanine-entangled fibrils with a high degree of control over the self-assembly lifetime and mechanical properties. Further, under acidic pH, the compound formed the O–H….O=C hydrogen-bonded dimer. The dimers were further self-assembled by intermolecular N–H….O=C hydrogen bonds and π–π stacking interactions to form fibrils with high mechanical properties, from this simple molecule. However, the self-assembly process is dynamic. Hence, the in situ generated NH3 uniformly increased the pH and led to the homogeneous disassembly of the fibrils. Thus, this report provides a valuable approach to defibrillation. Nature operates out of equilibrium, which needs a continuous input of energy. However, on the removal of the energy source, the system returns to its thermodynamically stable building blocks, resulting in an aggregation-to-non aggregation transition. The control of this system is governed by kinetics. Herein, we have alleviated that system using a supramolecular gelator with dynamic covalent bonds. In the aqueous solution of benzyloxycarbonyl-L-phenylalanine (ZF), equilibrium self-assembly and gelation take place at 4 mg/mL; however, on the addition of 1-ethyl-3-(3-(dimethylamino)propyl)carbodiimide (EDC), nonequilibrium hydrogels are formed at 2 mg/mL due to anhydride formation and self-assembly. However, with time, the hydrolysis of anhydride results in a gel-to-sol transition. The dynamic covalent bond formation and rupture have programmed the dissipative, transient supramolecular hydrogels from ZF with a high degree of control over the self-assembly lifetime. The system is not fully dissipative as it does not spontaneously oscillate between two states, but needs fuel to undergo a transition. The refueling of the system with EDC helps to access multiple cycles. Tryptophan-mediated photo cleavage of disulfide bonds and the resulting defibrillation process have been demonstrated. A supramolecular fiber-like network structure arises due to the self-assembly of dibenzyloxycarbonyl-L-cystine by non-covalent interactions such as hydrogen bonding, π–π interactions and hydrophobic effects. The entangled fiber network encapsulates water and forms a hydrogel. The hydrogel is thixotropic in nature and responsive to external stimuli like heat and pH. However, on UV irradiation, Trp-mediated disulfide bond cleavage occurs, leading to defibrillation and a gel-to-sol transition. The fiber is amyloid-like and exhibited positive results in the Congo red assay. But the sol does not respond to the Congo red assay. Ellman’s test further confirmed the photo-induced cystine to cysteine conversion. In the presence of Ellman’s reagent, on UV exposure of the DZC hydrogel, a sharp absorption intensity at 412 nm occurs due to the reaction of newly generated thiolate anions from DZC with 5,5’-dithiobis-(2-nitrobenzoic acid) (DTNB). Organic-inorganic hybrid materials are highly important for designing and engineering bioinspired structures and functions. Herein, we have demonstrated mineralization-induced gelation of triazole-appended phenylalanine and resulting stiffness enhancement of the hydrogel. The 2,5-diphenyl-2H-[1,2,3]triazole-4-carboxylic acid was coupled with L-Phe to develop the hydrogelator. Starting with basic (pH 11) solutions (5 mg/mL) of gelators functionalized with the 1,2,3- triazole group, we show that significant stiffness enhancement is achieved upon adding Ca+2. From rheology, the storage modulus exhibits 8 fold increase by the mineralization, which enhance further by heating. The hydrogels are thixotropic. The mineralization process has been exploited as a strategy to induce physical cross-links and bundling of gel fibers, which not only influences the gel microstructure but also manipulates subsequent mechanical properties of the hydrogels. We have designed and synthesized , hybrid peptide luminophore with conformationally rigid 2-amino-4-methyl-thiazole-5-carboxylic acid ethyl ester and flexible L-phenylalanine to study the structure, self-assembly and optical response. The 2-amino-4-methyl-thiazole-5-carboxylic acid ethyl ester was synthesized by refluxing 2-bromo-ethylacetoacetate and thiourea in ethanol. From single crystal X-ray analysis, the hybrid peptide adopts an extended conformation stabilized by a S….O=C interaction. The hybrid peptide self-assembled to form an anti-parallel sheet-like structure stabilized by multiple intermolecular hydrogen bonds. Moreover, the anti-parallel sheet-like structure is also stabilized by two edge-to-edge π–π stacking interactions. In higher order packing, it forms a complex sheet-like structure. Moreover, the , hybrid peptide sheet shows birefringence under polarized light and blue emission on excitation at 340 nm and behave like optical waveguide. The , hybrid peptide sheet further assembled to form micro flower-like morphology from EtOH-H2O solution, as depicted by FE-SEM. Phenylalanine derivatives are extremely useful in developing functional materials with special optoelectronic properties for diverse applications in future biotechnology, nanotechnology, medicine, material science and chemistry. However, designing synergistically aggregated building blocks to produce tailor-made functional nanomaterial is still challenging. We describe fibrils of aromatically altered peptide that effectively delocalize electrons. Under varied circumstances, polymorphic fibril products with distinctly varying conductivities were created by peptide self-assembly. We have developed nanotubes by solvent-induced polymorph transformation of a phenylalanine derivative. Using diverse experimental techniques, we demonstrate that compared to EtOH and EtOH/water, ACN and ACN/water induce nanotubes exhibit excellent conductivity and piezoelectric properties. The ACN or ACN/water solutions assembly is mainly governed by hydrogen bonding and π-stacking interactions, favoring -sheet formation and leading to long fibrils. The output open-circuit voltage (Voc) for the device reached 2.4 V under an applied force of 40 N, comparable to those produced with nanogenerators made up of organic polymers or inorganic materials. Thus, the functionality of a system can be fine-tuned by carefully managing polymorphisms by selecting appropriate environmental assembly circumstances. This technique enables the detailed characterization of several polymorphs and allows for the establishment of conditions that result in the polymorph with the highest conductivity.

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